NTR: retinal ganglion cell axon formation+regn terms

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Hi,

For annotation of Pax2_mouse (P32114 ) in PMID:18083586 (IMP), I have just created the following terms via Term Genie (id: GO:2000595 name: regulation of optic nerve formation; id: GO:2000596 name: negative regulation of optic nerve formation; id: GO:2000597 name: positive regulation of optic nerve formation) but thought I could be a bit more specific since the optic nerve is composed of retinal ganglion cell axons and support cells Wikipaedia (http://en.wikipedia.org/wiki/Optic\_nerve)! Hence, although the paper refers to optic nerve axons please may a request the following new term (which are in line with the cell type ontology CL:0000740 retinal ganglion cell):

GO:0021634 optic nerve formation --<GO:NEW optic nerve axon formation --< GONEW retinal ganglion cell axon formation --<GO:NEW regulation of retinal ganglion cell axon formation --<GO:NEW positive regulation of retinal ganglion cell axon formation (IMP) --< GO:NEW negative regulation of retinal ganglion cell axon formation

Thanks, Yasmin

Reported by: yafaruque

Original Ticket: geneontology/ontology-requests/8360

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• assigned_to: nobody --> paolaroncaglia

Original comment by: paolaroncaglia

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Hi Yasmin,

Summing up from the Wikipedia pages on optic nerve and retinal ganglion cell:

The optic nerve is composed of retinal ganglion cell axons and support cells. Each optic nerve contains around 1.2 million nerve fibers, which are axons of the retinal ganglion cells of one retina. Retinal ganglion cells vary significantly in terms of their size, connections, and responses to visual stimulation but they all share the defining property of having a long axon that extends into the brain. These axons form the optic nerve, optic chiasm, and optic tract.

So when your paper refers to optic nerve axon number, it's actually referring to the axons of the ganglion cells. Nerves don't have axons; neurons do. So in GO we clearly define GO:0030424 axon as the projection of a neuron, not of a nerve. See also a recent SourceForge item by Alex Diehl: https://sourceforge.net/tracker/?func=detail&aid=3285412&group\_id=36855&atid=440764

Therefore, the term GO:0021634 optic nerve formation --<GO:NEW optic nerve axon formation would be incorrect.

The term GO:0021634 optic nerve formation --< GONEW retinal ganglion cell axon formation if created, should be a child of GO:0007409 axonogenesis, similarly to how GO:0031290 retinal ganglion cell axon guidance is_a GO:0007411 axon guidance and should have a Dbxref to link it to retinal ganglion cell in the cell type ontology.

As for your annotations, however, the authors conclude by postulating that "a lack of structural and trophic support normally provided by glial cells and/or aberrant cell–cell interactions in PAX2-deficient mice leads to early death of a population of ganglion cells and a resultant decrease in optic nerve axons." That is, the regulation of axon numbers they observe by Pax2 is likely due to a regulation of the ganglion cell number, and not to a regulation of retinal ganglion cell axon formation. Therefore, I'd leave the annotations as you have them, i.e. simply referring to optic nerve formation.

Thanks, Paola

Original comment by: paolaroncaglia

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• status: open --> closed-rejected

Original comment by: paolaroncaglia

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Hi Paola, thanks for the explanation - I will leave my annotations as they are then, chhers, Yasmin

Original comment by: yafaruque

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To the GO editors and other interested parties:

As an aside, at the CL-INCF neuron meeting in April, it was agreed that INCF would sponsor a one-day satellite meeting on Wednesday September 7, directly following the INCF Neuroinformatics 2011 meeting in Boston for the purpose of bringing together GO ontology developers and neuroscientists to discuss and improve GO terms related to neuroscience.

I will be organizing this meeting and would request that GO editors collect a list of potential terms and areas in neuroscience that we might work on. Simple term requests should of course go forward as always, but terms that might benefit from direct input from neuroscientists should be noted. More information will be forthcoming shortly.

Thanks,

Alex

Original comment by: addiehl

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Thanks Alex, I'll forward the info and we'll certainly be in touch about this. Paola

Original comment by: paolaroncaglia

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• labels: 390929 --> neurobiology

Original comment by: paolaroncaglia